The clip is supposed to look warped. its not perfectly round. Grab the outer end of the axle and push in on it. The CV joints slide in and out to allow for length changes during suspension articulation and steering. Now, slide the axle into the transmission and do the same thing but do it like you're angry. Pound it in using that compression. Don't just push and wait, pound it. Slam those puppies home. If you're not afraid of knocking the car off the jackstands, you're not doing it hard enough
Don't take the boot off... there is no reason for it, and its a mess. Its full of a thin grease that is the consistency of sour cream.